It is actually very simple to discourage big players grouping together into one big guild. By simply giving a penalty for big guilds.

Example, if the guild has a 100% rep buff, and the guild has 100 members, it is divided evenly so that each member only has 1% rep buff.

Also, can introduce an upkeep cost for the big guilds. like a daily contribution tax/rep tax multiply by guild level to stay in a guild.

You can think of many other ways too not limited to the above. This is the basic mechanism for game balancing, by boosting weaker players/guilds and penalizing bigger players/guild to a certain degree so that the gameplay evolves and gets more interesing